Burning Mouth Syndrome (BMS) is a multifactorial, chronic pain condition with neuropathic and psychogenic mechanisms. Cortical activation as well as sustained attention and executive functions have proven to be affected by chronic pain. The main objectives of this work were to test the efficacy of a multidimensional personalized pain treatment protocol and to investigate if the effects are based on psychophysical pain processing changes or cognitive effects. A 74-year-old female with 2 years of BMS received 10 sessions of a combined protocol of anodal left dorsolateral prefrontal cortex tDCS, cognitive therapy, and therapeutic exercise. The subjective perception of pain decreased by 47% after treatment but returned to the baseline at 45 days. No changes were found in objective pain measurements apart from a transient worsening of conditioned pain modulation. A large effect size was found in all functional scales, processing speed and executive control as well as sustained attention that persisted during follow-up. No changes in anxiety and depression were found. A multimodal therapeutic approach combining TDCS, cognitive rehabilitation and therapeutic exercise produces improved quality of life, disability and pain perception correlated with improvements in processing speed, executive control and sustained attention but independent of changes in psychophysical pain processing.